Paper Citing NAMD - Abstract
Wierzbicki, Andrzej; Dalal, Pranav; Cheatham, Thomas E., I.I.I.; Knickelbein, Jared E.; Haymet, A. D. J.; Madura, Jeffry D.
Antifreeze proteins at the Ice/Water interface: Three calculated discriminating properties for orientation of type I proteins
BIOPHYSICAL JOURNAL, 93:1442-1451, SEP 2007
Antifreeze proteins (AFPs) protect many plants and organisms from freezing in low temperatures. Of the different AFPs, the most studied AFP Type I from winter flounder is used in the current computational studies to gain molecular insight into its adsorption at the ice/water interface. Employing molecular dynamics simulations, we calculate the free energy difference between the hydrophilic and hydrophobic faces of the protein interacting with ice. Furthermore, we identify three properties of Type I "antifreeze'' proteins that discriminate among these two orientations of the protein at the ice/water interface. The three properties are: the "surface area'' of the protein; a measure of the interaction of the protein with neighboring water molecules as determined by the number of hydrogen bond count, for example; and the side-chain orientation angles of the threonine residues. All three discriminants are consistent with our free energy results, which clearly show that the hydrophilic protein face orientations toward the ice/water interface, as hypothesized from experimental and ice/vacuum simulations, are incorrect and support the hypothesis that the hydrophobic face is oriented toward the ice/water interface. The adsorption free energy is calculated to be 2-3 kJ/ mol.
